Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate BPHYT_RS05030 BPHYT_RS05030 sugar ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__BFirm:BPHYT_RS05030 Length = 312 Score = 375 bits (963), Expect = e-109 Identities = 177/300 (59%), Positives = 231/300 (77%), Gaps = 1/300 (0%) Query: 3 SVAVFSKASPFDAL-QRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVG 61 + V +ASP AL RW+PKLVLAPS++I L+ YG+I T LS +NS MP Y++VG Sbjct: 11 TATVTRRASPMAALADRWIPKLVLAPSVVISLIFVYGFIAITGYLSLSNSRLMPRYEFVG 70 Query: 62 LQQYMRLMDNDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPM 121 L +Y L DND +W ++ NL FG FI + + LG+FLA+LLDQ+IR EG +R V+LYPM Sbjct: 71 LDRYRELFDNDVFWTSAANLGWFGIPFIGVCIGLGLFLAILLDQQIRNEGALRAVFLYPM 130 Query: 122 ALSMIVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFV 181 ALS IVTGTAW+W++ P +GL+K+ DWGW F WL D D+ ++C+VIAAVWQ++GFV Sbjct: 131 ALSFIVTGTAWQWIMTPSIGLEKVFHDWGWTSFSFSWLGDPDKAIFCVVIAAVWQSTGFV 190 Query: 182 MAMFLAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLV 241 MA+FLAGLRGVD I +AAQ+DGA LPTIY KIV+PS+RPVFFS +IL HI IK+FDLV Sbjct: 191 MALFLAGLRGVDGEIFKAAQMDGAGLPTIYRKIVIPSMRPVFFSVLLILCHITIKTFDLV 250 Query: 242 AAMTAGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKRH 301 A+TAGGPG SS LPA+FMY+F+F+RGQ+G+G+AS+M+ML V+ +LVP +Y E R R+ Sbjct: 251 VALTAGGPGTSSSLPAIFMYTFSFNRGQLGVGAASSMMMLATVVAVLVPLMYLESRSTRN 310 Lambda K H 0.329 0.141 0.448 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 394 Number of extensions: 13 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 302 Length of database: 312 Length adjustment: 27 Effective length of query: 275 Effective length of database: 285 Effective search space: 78375 Effective search space used: 78375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory